229 research outputs found
Role of Quantum Coherence and Energetic Disorder on Exciton Transport in Polymer Films
The cross-over from coherent to incoherent exciton transport in disordered
polymer films is studied by computationally solving a modified form of the
Redfield equation for the exciton density matrix. This theory models quantum
mechanical (ballistic) and incoherent (diffusive) transport as limiting cases.
It also reproduces Forster transport for certain parameter regimes. Using model
parameters appropriate to polymer thin films it is shown that short-time
quantum mechanical coherence increases the exciton diffusion length. It also
causes rapid initial energy relaxation and larger line widths. The route to
equilibrium is, however, more questionable, as the equilibrium populations of
the model do not satisfy the Boltzmann distributions over the site energies.
The Redfield equation for the dimer is solved exactly to provide insight into
the numerical results.Comment: Accepted for publication in Phys. Rev. B. (July 2006). 19 pages and 8
figure
Thermodynamic limits on oxygenic photosynthesis around M-dwarf stars: Generalized models and strategies for optimization
We explore the feasibility and potential characteristics of photosynthetic
light-harvesting on exo-planets orbiting in the habitable zone of low mass
stars ( M). As stellar temperature, , decreases, the
irradiance maximum red-shifts out of the
nm range of wavelengths that can be utilized by \emph{oxygenic} photosynthesis
on Earth. However, limited irradiance in this region does not preclude oxygenic
photosynthesis and Earth's plants, algae and cyanobacteria all possess very
efficient \emph{light-harvesting antennae} that facilitate photosynthesis in
very low light. Here we construct general models of photosynthetic
light-harvesting structures to determine how an oxygenic photosystem would
perform in different irradiant spectral fluxes. We illustrate that the process
of light-harvesting, capturing energy over a large antenna and concentrating it
into a small \emph{reaction centre}, must overcome a fundamental \emph{entropic
barrier}. We show that a plant-like antenna cannot be adapted to the light from
stars of K, as increasing antenna size offers diminishing returns
on light-harvesting. This can be overcome if one introduces a slight
\emph{enthalpic gradient}, to the antenna. Interestingly, this strategy appears
to have been adopted by Earth's oxygenic cyanobacteria, and we conclude that
\emph{bacterial} oxygenic photosynthesis is feasible around even the lowest
mass M-dwarf stars.Comment: 5 Figures, submitted to Astrobiology and awaiting return of revie
Halo mass - concentration relation from weak lensing
We perform a statistical weak lensing analysis of dark matter profiles around
tracers of halo mass from galactic- to cluster-size halos. In this analysis we
use 170,640 isolated ~L* galaxies split into ellipticals and spirals, 38,236
groups traced by isolated spectroscopic Luminous Red Galaxies (LRGs) and 13,823
MaxBCG clusters from the Sloan Digital Sky Survey (SDSS) covering a wide range
of richness. Together these three samples allow a determination of the density
profiles of dark matter halos over three orders of magnitude in mass, from
10^{12} M_{sun} to 10^{15} M_{sun}. The resulting lensing signal is consistent
with an NFW or Einasto profile on scales outside the central region. We find
that the NFW concentration parameter c_{200b} decreases with halo mass, from
around 10 for galactic halos to 4 for cluster halos. Assuming its dependence on
halo mass in the form of c_{200b} = c_0 [M/(10^{14}M_{sun}/h)]^{\beta}, we find
c_0=4.6 +/- 0.7 (at z=0.22) and \beta=0.13 +/- 0.07, with very similar results
for the Einasto profile. The slope (\beta) is in agreement with theoretical
predictions, while the amplitude is about two standard deviations below the
predictions for this mass and redshift, but we note that the published values
in the literature differ at a level of 10-20% and that for a proper comparison
our analysis should be repeated in simulations. We discuss the implications of
our results for the baryonic effects on the shear power spectrum: since these
are expected to increase the halo concentration, the fact that we see no
evidence of high concentrations on scales above 20% of the virial radius
suggests that baryonic effects are limited to small scales, and are not a
significant source of uncertainty for the current weak lensing measurements of
the dark matter power spectrum. [ABRIDGED]Comment: 17 pages, 5 figures, accepted to JCAP pending minor revisions that
are included in v2 here on arXi
Sunyaev Zel'dovich Effect Observations of Strong Lensing Galaxy Clusters: Probing the Over-Concentration Problem
We have measured the Sunyaev Zel'dovich (SZ) effect for a sample of ten
strong lensing selected galaxy clusters using the Sunyaev Zel'dovich Array
(SZA). The SZA is sensitive to structures on spatial scales of a few
arcminutes, while the strong lensing mass modeling constrains the mass at small
scales (typically < 30"). Combining the two provides information about the
projected concentrations of the strong lensing clusters. The Einstein radii we
measure are twice as large as expected given the masses inferred from SZ
scaling relations. A Monte Carlo simulation indicates that a sample randomly
drawn from the expected distribution would have a larger median Einstein radius
than the observed clusters about 3% of the time. The implied overconcentration
has been noted in previous studies with smaller samples of lensing clusters. It
persists for this sample, with the caveat that this could result from a
systematic effect such as if the gas fractions of the strong lensing clusters
are substantially below what is expected.Comment: submitte
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BioTIME: A database of biodiversity time series for the Anthropocene.
MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL
Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci
Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits
An Integrated Microfluidic Device for Monitoring Changes in Nitric Oxide Production in Single T-Lymphocyte (Jurkat) Cells
A considerable amount of attention has been focused on the analysis of single cells in an effort to better understand cell heterogeneity in cancer and neurodegenerative diseases. Although microfluidic devices have several advantages for single cell analysis, few papers have actually demonstrated the ability of these devices to monitor chemical changes in perturbed biological systems. In this paper, a new microfluidic channel manifold is described that integrates cell transport, lysis, injection, electrophoretic separation, and fluorescence detection into a single device, making it possible to analyze individual cells at a rate of 10 cells/min in an automated fashion. The system was employed to measure nitric oxide (NO) production in single T-lymphocytes (Jurkat cells) using a fluorescent marker, 4-amino-5-methylamino-2',7'-difluorofluorescein diacetate (DAF-FM DA). The cells were also labeled with 6-carboxyfluorescein diacetate (6-CFDA) as an internal standard. The NO production by control cells was compared to that of cells stimulated using lipopolysaccharide (LPS), which is known to cause the expression of inducible nitric oxide synthase (iNOS) in immune-type cells. Statistical analysis of the resulting electropherograms from a population of cells indicated a twofold increase in NO production in the induced cells. These results compare nicely to a recently published bulk cell analysis of NO
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
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